1XVT - JenaLib

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Title :   CRYSTAL STRUCTURE OF NATIVE CAIB IN COMPLEX WITH COENZYME A

Authors :   E. S. Rangarajan, Y. Li, P. Iannuzzi, M. Cygler, A. Matte

Date :   28 Oct 04 (Deposition) - 15 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Caib, Coa Transferase, Carnitine, Crotonobetainyl Coa, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. S. Rangarajan, Y. Li, P. Iannuzzi, M. Cygler, A. Matte
Crystal Structure Of Escherichia Coli Crotonobetainyl-Coa: Carnitine Coa-Transferase (Caib) And Its Complexes With Coa And Carnitinyl-Coa.
Biochemistry V. 44 5728 2005
PubMed-ID: 15823031 | Reference-DOI: 10.1021/BI047656F

Molecule 1
	Chains	:	A
	EC Number	:	2.8.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T1
	Expression System Strain	:	DL41 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CAIB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	COA	1	Ligand/Ion	COENZYME A
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 34)

No.	Name	Count	Type	Full Name
1	COA	2	Ligand/Ion	COENZYME A
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:23 , ILE A:24 , ALA A:25 , ASN A:45 , LEU A:71 , ASN A:72 , ILE A:73 , PHE A:74 , ALA A:95 , SER A:96 , LYS A:97 , ALA A:100 , ARG A:103 , ARG A:104 , PRO A:138 , ALA A:139 , ASP A:169 , ASN A:316 , HOH A:535 , HOH A:546	BINDING SITE FOR RESIDUE COA A 501

(no "SS Bond" information available for 1XVT)

Asymmetric Unit

No.	Residues
1	Phe A:164	-	Pro A:165
2	Mse A:357	-	Pro A:358

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAIB_ECOLI_001 *	V	187	A	CAIB_ECOLI	---	---	A	V	187	A
2	UniProt	VAR_CAIB_ECOLI_002 *	T	302	A	CAIB_ECOLI	---	---	A	T	302	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAIB_ECOLI_001 *	V	187	A	CAIB_ECOLI	---	---	A	V	187	A
2	UniProt	VAR_CAIB_ECOLI_002 *	T	302	A	CAIB_ECOLI	---	---	A	T	302	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1XVT)

(no "Exon" information available for 1XVT)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:402
 aligned with CAIB_ECOLI | P31572 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:402
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  
           CAIB_ECOLI     4 LPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED 405
               SCOP domains d1xvta_ A: Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1xvtA01 A:4-226,A:330-405 Crotonobetainyl-coa:carnitine coa-transferase; domain 1                                                                                                                                              1xvtA02 A:227-329 formyl-coa transferase, domain 3                                                     1xvtA01 A:4-226,A:330-405                                                    CATH domains
               Pfam domains -----------------------------------------------------------------CoA_transf_3-1xvtA01 A:69-258                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhh..eeeeee.....hhhhhh..hhhhhh...eeee....hhhhhhhhhhhhh...eeeee...hhhhhh..hhhhhhhhh...eeeeee...............hhhhhhhhh.hhhh.ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..................eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh..hhhhhhhhhhhhh.eeee..hhhhh..hhhhhhh..eeeee.....eeeee......................hhhhhhhh...hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xvt A   4 LPmPKFGPLAGLRVVFSGIEIAGPFAGQmFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLmETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPmPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAmYEVmLRmGQYFmmDYFNGGEmCPRmSKGKDPYYAGCGLYKCADGYIVmELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTmDGRTCKGPNImPKFKNNPGQIWRGmPSHGmDTAAILKNIGYSENDIQELVSKGLAKVED 405
                              |     13        23        33        43        53        63        73        83  |     93       103       113       123       133       143       153       163       173       183       193      |203|  |   213       223 |     233       243    |  253       263       273       283       293       303       313       323       333       343  |    353   |   363       373  |    383       393       403  
                              |                        32-MSE                                                86-MSE                                                                    161-MSE                                200-MSE  |    ||     221-MSE                    248-MSE                                                                                           346-MSE    357-MSE       371-MSE|                             
                              6-MSE                                                                                                                                                                                               204-MSE   ||         225-MSE                                                                                                                                                376-MSE                         
                                                                                                                                                                                                                                     207-MSE||                                                                                                                                                                                                
                                                                                                                                                                                                                                          212-MSE                                                                                                                                                                                             
                                                                                                                                                                                                                                           213-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CoA_transf_3] (25)

Family: CoA_transf_3 (25)

Escherichia coli (strain K12) (13)

CoA_transf_3-1xvtA01

A:69-258

Asymmetric Unit(hide GO term definitions)

Chain A (CAIB_ECOLI | P31572)

molecular function
	GO:0008410	CoA-transferase activity	Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).
	GO:0008735	carnitine dehydratase activity	Catalysis of the reaction: (R)-carnitine = crotono-betaine + H(2)O.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016782	transferase activity, transferring sulfur-containing groups	Catalysis of the transfer of a sulfur-containing group from one compound (donor) to another (acceptor).
biological process
	GO:0042413	carnitine catabolic process	The chemical reactions and pathways resulting in the breakdown of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
	GO:0009437	carnitine metabolic process	The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Mse A:357 - Pro A:358	[ RasMol ]
		Phe A:164 - Pro A:165	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	1xvt
		Family and Domain Information	:	ProDom \| SYSTERS
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	CAIB_ECOLI \| P31572
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	2.8.3.-
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	CAIB_ECOLI \| P31572
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UniProtKB/Swiss-Prot
	CAIB_ECOLI \| P31572	:	1xa3 1xa4 1xk6 1xk7 1xvu 1xvv

1xk6	NATIVE PROTEIN IN P1 FORM
1xk7	NATIVE PROTEIN IN C2 FORM
1xvu	D169A MUTANT IN COMPLEX WITH COENZYME A
1xvv	CRYSTAL STRUCTURE OF CAIB MUTANT D169A IN COMPLEX WITH CARNITYL-COA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (2, 2)

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Gene Ontology (8, 8)

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